To close this out -we discovered that our problem was with Jaguars that actually had an older firmware (v85!). Apparently that version was not pwm friendly at all. Upgrading the firmware resolved the issue.
Sorry for the misguided report - this was on our 2009 robot, and my understanding that all the Jags had been updated to v89 was incorrect.
Thanks to everyone who confirmed things working as intended.
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I didn't know that heart beat was a (persistently) configurable option.
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BTW -- Before noticing the firmware downrev, I tried toggling this option. It only seems to modify if heartbeat is send over CAN by bdc-comm at that present time. It does not seem to be a persistent option that modifies Jaguar operation.